+Open data
-Basic information
Entry | Database: PDB / ID: 4yto | ||||||
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Title | Structure of coiled-coil domain of SYCP1 | ||||||
Components | Synaptonemal complex protein 1 | ||||||
Keywords | CELL CYCLE / coiled-coil domain / Syneptonemal complex / SYCP1 | ||||||
Function / homology | Function and homology information transverse filament / lateral element assembly / meiotic DNA repair synthesis / chiasma assembly / autosome / central element / sperm DNA condensation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex ...transverse filament / lateral element assembly / meiotic DNA repair synthesis / chiasma assembly / autosome / central element / sperm DNA condensation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / reciprocal meiotic recombination / chromosome, centromeric region / Meiotic synapsis / male germ cell nucleus / regulation of protein localization / chromosome / spermatogenesis / double-stranded DNA binding / protein homotetramerization / cell division / DNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | park, H.H. | ||||||
Citation | Journal: To Be Published Title: Structure of coiled-coil domain of SYCP1 Authors: Park, H.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yto.cif.gz | 54 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yto.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 4yto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yto_validation.pdf.gz | 448.1 KB | Display | wwPDB validaton report |
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Full document | 4yto_full_validation.pdf.gz | 452.4 KB | Display | |
Data in XML | 4yto_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 4yto_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/4yto ftp://data.pdbj.org/pub/pdb/validation_reports/yt/4yto | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17646.160 Da / Num. of mol.: 2 / Fragment: UNP residues 662-801 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SYCP1, SCP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15431 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: ammonium chloride, 0.1 M sodium acetate / PH range: 4.6 - 5.0 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 39027 / % possible obs: 97.5 % / Redundancy: 7 % / Net I/σ(I): 30 |
-Processing
Software |
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Refinement | Resolution: 2→28.19 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.788 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.135 Å2
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Refinement step | Cycle: 1 / Resolution: 2→28.19 Å
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Refine LS restraints |
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